Many studies in coastal areas have shown the existence of thin chemical and biological layers. Their thickness and vertical extension are mainly controlled by hydrological and physical forcing. An accurate description of the phytoplankton communities growing within these layers is difficult to obtain without a well-adapted sampling system. A new Fine Scale Sampler (FSS) has been designed in Ifremer in order to study phytoplankton distribution and associated dissolved properties in high stratified water column. This FSS consists in a vertical array of 15 sampling bottles, horizontally laid with 20 cm intervals. Data acquired from a CTD and Fluorescence probe provide a precise FSS positioning at the depth of highest density gradient or at chlorophyll a maximum. For two seasonal situations (spring and summer), the FSS allowed us to investigate micro-scale vertical distribution of phytoplankton species and relationships with physico-chemical parameters in the Loire estuary. For both situation, it was shown that the vertical distribution of phytoplankton communities was very variable. In summer conditions, the diatom Chaetoceros sociale was dominant in the phytoplankton peak located below the pycnocline and a thin layer of Dinophysis acuminata was detected 1 m above, in nutrient depleted conditions.